PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
|
Home TFext BLAST Prediction Download Help About Links PlantRegMap |
Transcription Factor Information
Basic Information? help Back to Top | |||||||||
---|---|---|---|---|---|---|---|---|---|
TF ID | GSVIVT01020612001 | ||||||||
Common Name | VIT_12s0028g03030 | ||||||||
Organism | |||||||||
Taxonomic ID | |||||||||
Taxonomic Lineage |
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; rosids incertae sedis; Vitales; Vitaceae; Vitis
|
||||||||
Family | C2H2 | ||||||||
Protein Properties | Length: 428aa MW: 47173.2 Da PI: 9.4518 | ||||||||
Description | C2H2 family protein | ||||||||
Gene Model |
|
Signature Domain? help Back to Top | |||||||
---|---|---|---|---|---|---|---|
No. | Domain | Score | E-value | Start | End | HMM Start | HMM End |
1 | zf-C2H2 | 15.9 | 3.7e-05 | 59 | 79 | 3 | 23 |
ETTTTEEESSHHHHHHHHHHT CS zf-C2H2 3 CpdCgksFsrksnLkrHirtH 23 C++Cgk F r nL+ H r H GSVIVT01020612001 59 CEICGKGFQRDQNLQLHRRGH 79 *******************88 PP | |||||||
2 | zf-C2H2 | 14.8 | 8.1e-05 | 133 | 155 | 1 | 23 |
EEETTTTEEESSHHHHHHHHHHT CS zf-C2H2 1 ykCpdCgksFsrksnLkrHirtH 23 +kC++C+k++ +s+ k H +t+ GSVIVT01020612001 133 WKCEKCSKRYAVQSDWKAHTKTC 155 58*******************98 PP |
Protein Features ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Database | Entry ID | E-value | Start | End | InterPro ID | Description |
Gene3D | G3DSA:3.30.160.60 | 3.6E-5 | 56 | 79 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 1.9E-6 | 56 | 79 | No hit | No description |
PROSITE profile | PS50157 | 11.489 | 57 | 79 | IPR007087 | Zinc finger, C2H2 |
SMART | SM00355 | 0.076 | 57 | 79 | IPR015880 | Zinc finger, C2H2-like |
PROSITE pattern | PS00028 | 0 | 59 | 79 | IPR007087 | Zinc finger, C2H2 |
Gene3D | G3DSA:3.30.160.60 | 1.6E-4 | 121 | 154 | IPR013087 | Zinc finger C2H2-type/integrase DNA-binding domain |
SuperFamily | SSF57667 | 1.9E-6 | 128 | 153 | No hit | No description |
SMART | SM00355 | 120 | 133 | 153 | IPR015880 | Zinc finger, C2H2-like |
Gene Ontology ? help Back to Top | ||||||
---|---|---|---|---|---|---|
GO Term | GO Category | GO Description | ||||
GO:0005634 | Cellular Component | nucleus | ||||
GO:0044212 | Molecular Function | transcription regulatory region DNA binding | ||||
GO:0046872 | Molecular Function | metal ion binding |
Sequence ? help Back to Top |
---|
Protein Sequence Length: 428 aa Download sequence Send to blast |
MLQKMAAEAI PNGFIQNPIG GSNPPTIKKK RNLPGTPDPE AEVIALSPKT LMATNRFLCE 60 ICGKGFQRDQ NLQLHRRGHN LPWKLKQRSS KEPRKRVYVC PEKTCVHHHP SRALGDLTGI 120 KKHFCRKHGE KKWKCEKCSK RYAVQSDWKA HTKTCGTREY KCDCGTLFSR RDSFITHRAF 180 CDALAEETAR VTAASNINNG TINYHFMGTS LAPSMPQHFS SIFKPISSND EATDQTRRGL 240 SLWMGQGSQG HETMGTNLQE IHQLRSSMSP GSSSNNTEDQ LTSSTSLPLS NVKEAAGSQI 300 VSVPSLYSSQ HHSHQTPLGN MSATALLQKA AQMGATSADP FLGSFGLKCD SSLVQDGNKF 360 CGLYTANQLP TNDMENPKDL STFNQLQMYP AKRRNTQNDD STGGQTRDFL GVGVQTICHP 420 SSINGWM* |
3D Structure ? help Back to Top | ||||||
---|---|---|---|---|---|---|
PDB ID | Evalue | Query Start | Query End | Hit Start | Hit End | Description |
5b3h_C | 1e-37 | 129 | 198 | 3 | 72 | Zinc finger protein JACKDAW |
5b3h_F | 1e-37 | 129 | 198 | 3 | 72 | Zinc finger protein JACKDAW |
Search in ModeBase |
Expression -- Description ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | Description | |||||
Uniprot | TISSUE SPECIFICITY: Expressed in the ground tissue and stele cells of embryos and 2-days post-germination roots but not in the quiescent center (PubMed:17785527). Detected only in cells that perform asymmetric cell divisions (PubMed:17785527). In roots, present in cortex, endodermis, and pericycle layer (PubMed:25829440). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:25829440}. |
Functional Description ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | Description | |||||
UniProt | Transcription factor that regulates tissue boundaries and asymmetric cell division (PubMed:17785527, PubMed:25829440). Contributes to the sequestration of 'SHORT-ROOT' to the nucleus (PubMed:17785527, PubMed:25829440). Interacts with the SCR and MGP promoters (PubMed:21935722). Does not show transcription activity by itself, but regulates the transcription of downstream genes through interaction with other transcription factors (PubMed:21935722). Binds DNA via its zinc fingers (PubMed:24821766). Recognizes and binds to SCL3 promoter sequence 5'-AGACAA-3' to promotes its expression when in complex with RGA (PubMed:24821766). Positively involved in gibberellic acid (GA) signaling (PubMed:24821766). {ECO:0000269|PubMed:17785527, ECO:0000269|PubMed:21935722, ECO:0000269|PubMed:24821766, ECO:0000269|PubMed:25829440}. |
Binding Motif ? help Back to Top | |||
---|---|---|---|
Motif ID | Method | Source | Motif file |
MP00125 | DAP | Transfer from AT1G03840 | Download |
Regulation -- Description ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | Description | |||||
UniProt | INDUCTION: Up-regulated by the transcription factor JKD, and down-regulated by SHR, SCR and itself. {ECO:0000269|PubMed:21935722}. |
Regulation -- PlantRegMap ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | Upstream Regulator | Target Gene | ||||
PlantRegMap | Retrieve | Retrieve |
Annotation -- Nucleotide ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Source | Hit ID | E-value | Description | |||
GenBank | AM425292 | 0.0 | AM425292.2 Vitis vinifera contig VV78X015037.17, whole genome shotgun sequence. |
Annotation -- Protein ? help Back to Top | |||||||
---|---|---|---|---|---|---|---|
Source | Hit ID | E-value | Description | ||||
Refseq | XP_002275400.3 | 0.0 | PREDICTED: zinc finger protein MAGPIE | ||||
Swissprot | Q9ZWA6 | 1e-152 | IDD3_ARATH; Zinc finger protein MAGPIE | ||||
TrEMBL | E0CTJ2 | 0.0 | E0CTJ2_VITVI; Uncharacterized protein | ||||
STRING | VIT_12s0028g03030.t01 | 0.0 | (Vitis vinifera) |
Orthologous Group ? help Back to Top | |||
---|---|---|---|
Lineage | Orthologous Group ID | Taxa Number | Gene Number |
Representative plant | OGRP95 | 16 | 242 |
Best hit in Arabidopsis thaliana ? help Back to Top | ||||||
---|---|---|---|---|---|---|
Hit ID | E-value | Description | ||||
AT1G03840.1 | 1e-153 | C2H2 family protein |
Link Out ? help Back to Top | |
---|---|
Phytozome | GSVIVT01020612001 |
Publications ? help Back to Top | |||
---|---|---|---|
|